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WDR74 rs11231247 contributes to the susceptibility and prognosis of non-small cell lung cancer. Pathol Res Pract 2023; 242:154318. [PMID: 36701849 DOI: 10.1016/j.prp.2023.154318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 01/03/2023] [Accepted: 01/16/2023] [Indexed: 01/22/2023]
Abstract
OBJECTIVES WD repeat-containing protein 74 (WDR74) has been linked with the development of lung cancer. This study aims to investigate the relationship between WDR74 rs11231247 and non-small cell lung cancer (NSCLC) susceptibility and the prognosis of NSCLC patients. METHODS UALCAN, MethPrimer, ensembl and Pancan meQTL databases were used for bioinformatics analysis. The case-control study included 462 NSCLC patients and 462 health controls. WDR74 rs11231247 genotype was determined by PCR-RFLP. Logistic regression model was used to calculate odds ratio (OR) and 95% confidence interval (95% CI) for analyzing the association of WDR74 SNP with the risk of NSCLC. Log-rank test and Cox regression analysis were used to evaluate the effect of WDR74 genetic variation on the prognosis of NSCLC. RESULTS Compared with normal tissues, WDR74 expression level was higher and methylation level was lower in LUAD tissues. There were two CpG islands presented in the promoter of WDR74. And rs11231247 was in the second CpG island. We then discovered that rs11231247 CC and CT were more likely modified by methylation. LUAD case-control study demonstrated that rs11231247 CC genotype was associated with NSCLC risk with OR (95%CI) of 5.29 (2.59-10.79). Stratified analysis showed that rs11231247 T > C polymorphism could increase NSCLC risk in younger subjects (age≤58) (OR = 1.64, 95%CI = 1.06-2.54, P = 0.027). Survival analysis and Cox regression analysis showed rs11231247 CC genotype contributed to a poor prognosis of NSCLC patients (MST=21, HR=2.09, 95%CI=1.17-3.75). CONCLUSION WDR74 rs11231247 polymorphism affected the risk and prognosis of NSCLC.
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Multi-omic characterization of genome-wide abnormal DNA methylation reveals diagnostic and prognostic markers for esophageal squamous-cell carcinoma. Signal Transduct Target Ther 2022; 7:53. [PMID: 35210398 PMCID: PMC8873499 DOI: 10.1038/s41392-022-00873-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 11/23/2021] [Accepted: 12/30/2021] [Indexed: 02/07/2023] Open
Abstract
This study investigates aberrant DNA methylations as potential diagnosis and prognosis markers for esophageal squamous-cell carcinoma (ESCC), which if diagnosed at advanced stages has <30% five-year survival rate. Comparing genome-wide methylation sites of 91 ESCC and matched adjacent normal tissues, we identified 35,577 differentially methylated CpG sites (DMCs) and characterized their distribution patterns. Integrating whole-genome DNA and RNA-sequencing data of the same samples, we found multiple dysregulated transcription factors and ESCC-specific genomic correlates of identified DMCs. Using featured DMCs, we developed a 12-marker diagnostic panel with high accuracy in our dataset and the TCGA ESCC dataset, and a 4-marker prognostic panel distinguishing high-risk patients. In-vitro experiments validated the functions of 4 marker host genes. Together these results provide additional evidence for the important roles of aberrant DNA methylations in ESCC development and progression. Our DMC-based diagnostic and prognostic panels have potential values for clinical care of ESCC, laying foundations for developing targeted methylation assays for future non-invasive cancer detection methods.
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Iqbal MA, Li M, Lin J, Zhang G, Chen M, Moazzam NF, Qian W. Preliminary Study on the Sequencing of Whole Genomic Methylation and Transcriptome-Related Genes in Thyroid Carcinoma. Cancers (Basel) 2022; 14:cancers14051163. [PMID: 35267472 PMCID: PMC8909391 DOI: 10.3390/cancers14051163] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 02/19/2022] [Accepted: 02/22/2022] [Indexed: 01/02/2023] Open
Abstract
Simple Summary Epigenetic alterations are critical for tumor onset and development. DNA methylation is one of the most studied pathways concerning various types of cancer. A promising and exciting avenue of research is the discovery of biomarkers of early-stage malignancies for disease prevention and prognostic indicators following cancer treatment by examining the DNA methylation modification of relevant genes implicated in cancer development. We have made significant advances in the study of DNA methylation and thyroid cancer. This study is novel in that it distinguished methylation changes that occurred primarily in the gene body region of the aforementioned hypermethylated or hypomethylated thyroid cancer genes. Our findings imply that exposing whole-genome DNA methylation patterns and gene expression profiles in thyroid cancer provides new insight into the carcinogenesis of thyroid cancer, demonstrating that gene expression mediated by DNA methylation modifications may play a significant role in tumor growth. Abstract Thyroid carcinoma is the most prevalent endocrine cancer globally and the primary cause of cancer-related mortality. Epigenetic modifications are progressively being linked to metastasis. This study aimed to examine whole-genome DNA methylation patterns and the gene expression profiles in thyroid cancer tissue samples using a MethylationEPIC BeadChip (850K), RNA sequencing, and a targeted bisulfite sequencing assay. The results of the Illumina Infinium human methylation kit (850K) analyses identified differentially methylated CpG locations (DMPs) and differentially methylated CpG regions (DMRs) encompassing nearly the entire genome with high resolution and depth. Gene ontology and KEGG pathway analyses revealed that the genes associated with DMRs belonged to various domain-specific ontologies, including cell adhesion, molecule binding, and proliferation. The RNA-Seq study found 1627 differentially expressed genes, 1174 of which that were up-regulated and 453 of which that were down-regulated. The targeted bisulfite sequencing assay revealed that CHST2, DPP4, DUSP6, ITGA2, SLC1A5, TIAM1, TNIK, and ABTB2 methylation levels were dramatically lowered in thyroid cancer patients when compared to the controls, but GALNTL6, HTR7, SPOCD1, and GRM5 methylation levels were significantly raised. Our study revealed that the whole-genome DNA methylation patterns and gene expression profiles in thyroid cancer shed new light on the tumorigenesis of thyroid cancer.
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Affiliation(s)
- Muhammad Asad Iqbal
- Department of Otolaryngology-Head & Neck Surgery, Affiliated People’s Hospital of Jiangsu University, Zhenjiang 212002, China;
| | - Mingyang Li
- Department of Basic Medical Sciences, Affiliated to School of Medicine, Jiangsu University, Zhenjiang 212002, China;
| | - Jiang Lin
- Laboratory Center, Affiliated People’s Hospital of Jiangsu University, Zhenjiang 212132, China;
| | - Guoliang Zhang
- Department of General Surgery, Affiliated People’s Hospital of Jiangsu University, Zhenjiang 212132, China;
| | - Miao Chen
- Department of Pathology, Affiliated People’s Hospital of Jiangsu University, Zhenjiang 212132, China;
| | | | - Wei Qian
- Department of Otolaryngology-Head & Neck Surgery, Affiliated People’s Hospital of Jiangsu University, Zhenjiang 212002, China;
- Correspondence: ; Tel.: +86-0511-88917833 or +86-1535-8586188
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Goldmann T, Schmitt B, Müller J, Kröger M, Scheufele S, Marwitz S, Nitschkowski D, Schneider MA, Meister M, Muley T, Thomas M, Kugler C, Rabe KF, Siebert R, Reck M, Ammerpohl O. DNA methylation profiles of bronchoscopic biopsies for the diagnosis of lung cancer. Clin Epigenetics 2021; 13:38. [PMID: 33596996 PMCID: PMC7890863 DOI: 10.1186/s13148-021-01024-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 02/07/2021] [Indexed: 11/10/2022] Open
Abstract
Background Lung cancer is the leading cause of cancer-related death in most western countries in both, males and females, accounting for roughly 20–25% of all cancer deaths. For choosing the most appropriate therapy regimen a definite diagnosis is a prerequisite. However, histological characterization of bronchoscopic biopsies particularly with low tumor cell content is often challenging. Therefore, this study aims at (a) determining the value of DNA methylation analysis applied to specimens obtained by bronchoscopic biopsy for the diagnosis of lung cancer and (b) at comparing aberrantly CpG loci identified in bronchoscopic biopsy with those identified by analyzing surgical specimens. Results We report the HumanMethylation450-based DNA methylation analysis of paired samples of bronchoscopic biopsy specimens either from the tumor side or from the contralateral tumor-free bronchus in 37 patients with definite lung cancer diagnosis and 18 patients with suspicious diagnosis. A differential DNA methylation analysis between both biopsy sites of patients with definite diagnosis identified 1303 loci. Even those samples were separated by the set of 1303 loci in which histopathological analysis could not unambiguously define the dignity. Further differential DNA methylation analyses distinguished between SCLC and NSCLC. We validated our results in an independent cohort of 40 primary lung cancers obtained by open surgical resection and their corresponding controls from the same patient as well as in publically available DNA methylation data from a TCGA cohort which could also be classified with high accuracy. Conclusions Considering that the prognosis correlates with tumor stage at time of diagnosis, early detection of lung cancer is vital and DNA methylation analysis might add valuable information to reliably characterize lung cancer even in histologically ambiguous sample material. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01024-6.
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Affiliation(s)
- Torsten Goldmann
- Pathology of the University Medical Center Schleswig-Holstein (UKSH), Campus Lübeck and the Research Center Borstel, Lübeck, Borstel, Germany.,Airway Research Center North, Member of the German Center for Lung Research (DZL), Grosshansdorf, Germany
| | | | - Julia Müller
- Pathology of the University Medical Center Schleswig-Holstein (UKSH), Campus Lübeck and the Research Center Borstel, Lübeck, Borstel, Germany
| | - Maren Kröger
- Institute of Human Genetics, University Medical Center Schleswig-Holstein (UKSH), Campus Kiel, Germany
| | - Swetlana Scheufele
- Institute of Human Genetics, University Medical Center Schleswig-Holstein (UKSH), Campus Kiel, Germany.,Airway Research Center North, Member of the German Center for Lung Research (DZL), Grosshansdorf, Germany
| | - Sebastian Marwitz
- Pathology of the University Medical Center Schleswig-Holstein (UKSH), Campus Lübeck and the Research Center Borstel, Lübeck, Borstel, Germany.,Airway Research Center North, Member of the German Center for Lung Research (DZL), Grosshansdorf, Germany
| | - Dörte Nitschkowski
- Pathology of the University Medical Center Schleswig-Holstein (UKSH), Campus Lübeck and the Research Center Borstel, Lübeck, Borstel, Germany.,Airway Research Center North, Member of the German Center for Lung Research (DZL), Grosshansdorf, Germany
| | - Marc A Schneider
- Translational Research Unit, Thoraxklinik at University Hospital Heidelberg, 69126, Heidelberg, Germany.,Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany
| | - Michael Meister
- Translational Research Unit, Thoraxklinik at University Hospital Heidelberg, 69126, Heidelberg, Germany.,Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany
| | - Thomas Muley
- Translational Research Unit, Thoraxklinik at University Hospital Heidelberg, 69126, Heidelberg, Germany.,Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany
| | - Michael Thomas
- Internistische Onkologie der Thoraxtumoren, Thoraxklinik im Universitätsklinikum Heidelberg, Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
| | | | - Klaus F Rabe
- LungenClinic Grosshansdorf, Grosshansdorf, Germany.,Airway Research Center North, Member of the German Center for Lung Research (DZL), Grosshansdorf, Germany
| | - Reiner Siebert
- Institute of Human Genetics, University Medical Center Ulm, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Martin Reck
- LungenClinic Grosshansdorf, Grosshansdorf, Germany.,Airway Research Center North, Member of the German Center for Lung Research (DZL), Grosshansdorf, Germany
| | - Ole Ammerpohl
- Institute of Human Genetics, University Medical Center Ulm, Albert-Einstein-Allee 11, 89081, Ulm, Germany. .,Airway Research Center North, Member of the German Center for Lung Research (DZL), Grosshansdorf, Germany.
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5
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Tan X, Zhang S, Gao H, He W, Xu M, Wu Q, Ni X, Jiang H. Hypermethylation of the PTTG1IP promoter leads to low expression in early-stage non-small cell lung cancer. Oncol Lett 2019; 18:1278-1286. [PMID: 31423188 PMCID: PMC6607221 DOI: 10.3892/ol.2019.10400] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 04/15/2019] [Indexed: 12/25/2022] Open
Abstract
Despite the clinical requirement for early diagnosis, the early events in lung cancer and their mechanisms are not fully understood. Pituitary tumor transforming gene 1 binding factor (PTTG1IP) is a tumor-associated gene; however, to the best of our knowledge, its association with lung cancer has not been reported. The present study analyzed PTTG1IP expression in early-stage non-small cell lung cancer (NSCLC) samples and investigated its epigenetic regulatory mechanisms. The results revealed that the mRNA level of PTTG1IP in NSCLC tissues was significantly downregulated by 43% compared with that in adjacent tissues. In addition, overexpression of this gene significantly inhibited cell proliferation. According to data from The Cancer Genome Atlas, a significant negative correlation was identified between the PTTG1IP gene methylation level and expression level in lung adenocarcinoma and lung squamous cell carcinoma cases. Reduced representation bisulfite sequencing (RRBS) analysis of six paired early-stage NSCLC tissue samples indicated that the CpG island shore of the PTTG1IP promoter is hypermethylated in lung cancer tissues, which was further validated in 12 paired early-stage NSCLC samples via bisulfite amplicon sequencing. Following treatment with 5-aza-2′-deoxycytidine to reduce DNA methylation in the promoter region, the PTTG1IP mRNA level increased, indicating that the PTTG1IP promoter DNA methylation level negatively regulates PTTG1IP transcription. In conclusion, in early-stage NSCLC, the PTTG1IP gene is regulated by DNA methylation in its promoter region, which may participate in the development and progression of lung cancer.
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Affiliation(s)
- Xiaoming Tan
- Department of Respiratory Disease, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, P.R. China
| | - Sufen Zhang
- NHC Key Laboratory of Reproduction Regulation, Shanghai Institute of Planned Parenthood Research, Fudan University, Shanghai 200032, P.R. China
| | - Huifang Gao
- NHC Key Laboratory of Reproduction Regulation, Shanghai Institute of Planned Parenthood Research, Fudan University, Shanghai 200032, P.R. China
| | - Wanhong He
- NHC Key Laboratory of Reproduction Regulation, Shanghai Institute of Planned Parenthood Research, Fudan University, Shanghai 200032, P.R. China
| | - Minjie Xu
- NHC Key Laboratory of Reproduction Regulation, Shanghai Institute of Planned Parenthood Research, Fudan University, Shanghai 200032, P.R. China
| | - Qihan Wu
- NHC Key Laboratory of Reproduction Regulation, Shanghai Institute of Planned Parenthood Research, Fudan University, Shanghai 200032, P.R. China
| | - Xiaohua Ni
- NHC Key Laboratory of Reproduction Regulation, Shanghai Institute of Planned Parenthood Research, Fudan University, Shanghai 200032, P.R. China
| | - Handong Jiang
- Department of Respiratory Disease, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, P.R. China
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Gao C, Zhuang J, Zhou C, Liu L, Liu C, Li H, Zhao M, Liu G, Sun C. Developing DNA methylation-based prognostic biomarkers of acute myeloid leukemia. J Cell Biochem 2018; 119:10041-10050. [PMID: 30171717 DOI: 10.1002/jcb.27336] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 06/26/2018] [Indexed: 12/21/2022]
Abstract
Acute myeloid leukemia (AML) is a heterogeneous clonal neoplasm characterized by complex genomic alterations. The incidence of AML increases with age, and most cases experience serious illness and poor prognosis. To explore the relationship between abnormal DNA methylation and the occurrence and development of AML based on the Gene Expression Database (GEO), this study extracted data related to methylation in AML and identified a methylated CpG site that was significantly different in terms of expression and distribution between the primary cells of AML patients, and hematopoietic stem/progenitor cells from normal bone marrow. To further investigate the differences caused by the dysfunction of methylation sites, bioinformatics analysis was used to screen methylation-related biomarkers, and the potential prognostic genes were selected by univariate and multivariate Cox proportional hazards regressions. Finally, five independent prognostic indicators were identified. In addition, these results provide new insight into the molecular mechanisms of methylation.
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Affiliation(s)
- Chundi Gao
- College of First Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Jing Zhuang
- Department of Oncology, Weifang Traditional Chinese Hospital, Weifang, Shandong, China.,Department of Oncology, Affilited Hospital of Weifang Medical University, Weifang, Shandong, China
| | - Chao Zhou
- Department of Oncology, Weifang Traditional Chinese Hospital, Weifang, Shandong, China.,Department of Oncology, Affilited Hospital of Weifang Medical University, Weifang, Shandong, China
| | - Lijuan Liu
- Department of Oncology, Weifang Traditional Chinese Hospital, Weifang, Shandong, China.,Department of Oncology, Affilited Hospital of Weifang Medical University, Weifang, Shandong, China
| | - Cun Liu
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Huayao Li
- College of First Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Minzhang Zhao
- School of Medicine, Shandong University, Jinan, China
| | - Gongxi Liu
- Department of Oncology, Weifang Traditional Chinese Hospital, Weifang, Shandong, China.,Department of Oncology, Affilited Hospital of Weifang Medical University, Weifang, Shandong, China
| | - Changgang Sun
- Department of Oncology, Weifang Traditional Chinese Hospital, Weifang, Shandong, China.,Department of Oncology, Affilited Hospital of Weifang Medical University, Weifang, Shandong, China
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7
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Huang X, Wu C, Fu Y, Guo L, Kong X, Cai H. Methylation analysis for multiple gene promoters in non-small cell lung cancers in high indoor air pollution region in China. Bull Cancer 2018; 105:746-754. [PMID: 30126609 DOI: 10.1016/j.bulcan.2018.05.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 04/08/2018] [Accepted: 05/11/2018] [Indexed: 12/13/2022]
Abstract
AIM The prevalence and mortality rates of lung cancer in Xuanwei, Yunnan, China, are the highest in the world. The severe indoor air pollution caused by smoky coals with high benzo (a)pyrene (BaP) and quartz levels is the main environmental factor. The aim of this study was to investigate methylation profiles of promoters in eight genes in primary non-small cell lung cancers (NSCLC) exposed to smoky coals. MATERIALS AND METHODS Candidate genes including CDKN2A, DLEC1, CDH1, DAPK, RUNX3, APC, WIF1 and MGMT were determined for the promoter methylation status using Nested methylation-specific PCR (nMSP) in primary 23NSCLC tissues and in circulating tumor DNA (ctDNA) isolated from 42plasma samples (9matched to tissues) as well as 10healthy plasma samples, using Sanger sequencing to verify the results. RESULTS Seven of the 8genes, except MGMT, had relatively high methylation frequencies ranging from 39%-74% in tissues. Moreover, methylation frequencies in five genes identified in lung cancer plasma were 45% for CDKN2A, 48% for DLEC1, 76% for CDH1, 14% for DAPK, 29% for RUNX3, with a relatively good concordance of methylation among 9 tissues and paired plasma. However, the genes from all healthy plasma showed no methylation. CONCLUSIONS A panel of genes including CDKN2A, DLEC1, CDH1, DAPK and RUNX3 may be used as potential epigenetic biomarkers for early lung cancer detection. CDH1 promoter methylation was associated with lung cancer metastasis in areas of air pollution from buring of smoky coals. DLEC1 and CDH1 exhibited specific high methylation frequencies, different from previous reports.
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Affiliation(s)
- Xinwei Huang
- Kunming University of Science and Technology, Faculty of Environmental Science and Engineering, 650500 Kunming, Yunnan province, China; Kunming University of Science and Technology, Medical school, 650500 Kunming, Yunnan province, China; Kunming University of Science and Technology, Genetics and Pharmacogenomics Laboratory, 650500 Kunming, Yunnan province, China
| | - Chaoqun Wu
- Kunming University of Science and Technology, Medical school, 650500 Kunming, Yunnan province, China; Kunming University of Science and Technology, Genetics and Pharmacogenomics Laboratory, 650500 Kunming, Yunnan province, China
| | - Yu Fu
- Kunming University of Science and Technology, Medical school, 650500 Kunming, Yunnan province, China; Kunming University of Science and Technology, Genetics and Pharmacogenomics Laboratory, 650500 Kunming, Yunnan province, China
| | - Liqiong Guo
- Kunming University of Science and Technology, Medical school, 650500 Kunming, Yunnan province, China; Kunming University of Science and Technology, Genetics and Pharmacogenomics Laboratory, 650500 Kunming, Yunnan province, China
| | - Xiangyang Kong
- Kunming University of Science and Technology, Medical school, 650500 Kunming, Yunnan province, China; Kunming University of Science and Technology, Genetics and Pharmacogenomics Laboratory, 650500 Kunming, Yunnan province, China.
| | - Haibo Cai
- Yunfeng Hospital, Department of Oncology, 655400 Xuanwei City, Yunnan Province, China.
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8
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Kim DS, Lee WK, Park JY. Hypermethylation of normal mucosa of esophagus-specific 1 is associated with an unfavorable prognosis in patients with non-small cell lung cancer. Oncol Lett 2018; 16:2409-2415. [PMID: 30013631 PMCID: PMC6036558 DOI: 10.3892/ol.2018.8915] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 04/27/2018] [Indexed: 12/19/2022] Open
Abstract
Lung cancer is the leading cause of cancer-associated mortality due to high incidence and poor survival rates, irrespective of global variations in its biology and treatment. Changes in DNA methylation are frequent in cancer and constitute an important mechanism in tumorigenesis. Normal mucosa of esophagus-specific 1 (NMES1) is expressed in epithelial tissue and is believed to be a tumor suppressor gene. The present study investigated the methylation status of the NMES1 promoter in 178 cases of primary non-small cell lung cancer (NSCLC) by pyrosequencing and evaluated the prognostic value of this methylation. NMES1 methylation-positive tumors above the background threshold for non-malignant tissue were found in 15 cases (8.4%) and were detected exclusively in malignant tissues. In addition, univariate and multivariate analyses showed that methylation-positive patients experienced worse overall survival rate (OSR) compared with methylation-negative patients (adjusted hazard ratio, 2.62; 95% confidence interval, 1.20-5.69; P=0.02). Notably, within the methylation-positive group, patients with strong methylation tended to experience worse OSR compared with those with weak methylation (adjusted hazard ratio, 2.45 vs. 3.05; Ptrend=0.02). These findings suggest that NMES1 may serve an important role in lung cancer pathogenesis, and its methylation could be considered a prognostic marker for NSCLC. Further studies with large numbers of samples are required to confirm this conclusion.
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Affiliation(s)
- Dong Sun Kim
- Department of Anatomy, BK21 Plus KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu 702-422, Republic of Korea
| | - Won Kee Lee
- Department of Preventive Medicine, School of Medicine, Kyungpook National University, Daegu 702-422, Republic of Korea
| | - Jae Yong Park
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu 702-422, Republic of Korea
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Increased S100A15 expression and decreased DNA methylation of its gene promoter are involved in high metastasis potential and poor outcome of lung adenocarcinoma. Oncotarget 2018; 8:45710-45724. [PMID: 28498804 PMCID: PMC5542220 DOI: 10.18632/oncotarget.17391] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 04/10/2017] [Indexed: 01/02/2023] Open
Abstract
Purpose This study aims to determine the functional role of S100A15 and its promoter DNA methylation patterns in lung cancer progression. Experimental Design We analyzed 178 formalin-fixed paraffin embedded specimens from lung cancer patients, including 24 early stage and 91 advanced stage adenocarcinoma. S100A15 protein expression was evaluated by immunohistochemistry stain, and its DNA methylation levels were measured by pyrosequencing. Results S100A15 nuclear staining was increased in lung adenocarcinoma patients with distant metastasis versus those without distant metastasis. There was reduced one/three-year overall survival in adenocarcinoma patients receiving first line target therapy and harboring high nuclear expressions of S100A15. Both DNA methylation levels over -423 and -248 CpG sites of the S100A15 gene promoter were decreased in adenocarcinoma patients with distant metastasis, and the former was associated with lower one-year overall survival. The highly invasive CL1-5 cell lines display decreased DNA methylation over −412/−248/−56 CpG sites of the S100A15 gene promoter and increased S100A15 gene/protein expressions as compared with the less invasive CL1-0 cell lines. Knockdown of S100A15 in CL1-5 cell line inhibited cell proliferation, migration, and invasion, while over-expression of S100A15 in CL1-0 cell line promoted cell proliferation, migration, and invasion. RNA sequencing analysis revealed potential biological effects of S100A15 over-expression and knock-down with CTNNB1, ZEB1, CDC42, HSP90AA1, BST2, and PCNA being the pivotal down-stream mediators. Conclusions Increased S100A15 expression and decreased DNA methylation of its gene promoter region were associated with high metastasis potential and poor outcome in lung adenocarcinoma, probably through triggering CTNNB1 -centered pathways.
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Pu W, Wang C, Chen S, Zhao D, Zhou Y, Ma Y, Wang Y, Li C, Huang Z, Jin L, Guo S, Wang J, Wang M. Targeted bisulfite sequencing identified a panel of DNA methylation-based biomarkers for esophageal squamous cell carcinoma (ESCC). Clin Epigenetics 2017; 9:129. [PMID: 29270239 PMCID: PMC5732523 DOI: 10.1186/s13148-017-0430-7] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 11/29/2017] [Indexed: 12/20/2022] Open
Abstract
Background DNA methylation has been implicated as a promising biomarker for precise cancer diagnosis. However, limited DNA methylation-based biomarkers have been described in esophageal squamous cell carcinoma (ESCC). Methods A high-throughput DNA methylation dataset (100 samples) of ESCC from The Cancer Genome Atlas (TCGA) project was analyzed and validated along with another independent dataset (12 samples) from the Gene Expression Omnibus (GEO) database. The methylation status of peripheral blood mononuclear cells and peripheral blood leukocytes from healthy controls was also utilized for biomarker selection. The candidate CpG sites as well as their adjacent regions were further validated in 94 pairs of ESCC tumor and adjacent normal tissues from the Chinese Han population using the targeted bisulfite sequencing method. Logistic regression and several machine learning methods were applied for evaluation of the diagnostic ability of our panel. Results In the discovery stage, five hyper-methylated CpG sites were selected as candidate biomarkers for further analysis as shown below: cg15830431, P = 2.20 × 10−4; cg19396867, P = 3.60 × 10−4; cg20655070, P = 3.60 × 10−4; cg26671652, P = 5.77 × 10−4; and cg27062795, P = 3.60 × 10−4. In the validation stage, the methylation status of both the five CpG sites and their adjacent genomic regions were tested. The diagnostic model based on the combination of these five genomic regions yielded a robust performance (sensitivity = 0.75, specificity = 0.88, AUC = 0.85). Eight statistical models along with five-fold cross-validation were further applied, in which the SVM model reached the best accuracy in both training and test dataset (accuracy = 0.82 and 0.80, respectively). In addition, subgroup analyses revealed a significant difference in diagnostic performance between the alcohol use and non-alcohol use subgroups. Conclusions Methylation profiles of the five genomic regions covering cg15830431 (STK3), cg19396867, cg20655070, cg26671652 (ZNF418), and cg27062795 (ZNF542) can be used for effective methylation-based testing for ESCC diagnosis. Electronic supplementary material The online version of this article (10.1186/s13148-017-0430-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Weilin Pu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Chenji Wang
- Department of Biochemistry and Molecular Biology, Medical College, Soochow University, Suzhou, Jiangsu China
| | - Sidi Chen
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Dunmei Zhao
- Department of Biochemistry and Molecular Biology, Medical College, Soochow University, Suzhou, Jiangsu China
| | - Yinghui Zhou
- Department of Biochemistry and Molecular Biology, Medical College, Soochow University, Suzhou, Jiangsu China
| | - Yanyun Ma
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Ying Wang
- Genesky Biotechnologies Inc., Shanghai, China
| | - Caihua Li
- Genesky Biotechnologies Inc., Shanghai, China
| | - Zebin Huang
- Genesky Biotechnologies Inc., Shanghai, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Shicheng Guo
- Center for Human Genetics, Marshfield Clinic Research Foundation, 9500 Gilman Drive, MC0412, Marshfield, Wisconsin 54449 United States
| | - Jiucun Wang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Minghua Wang
- Department of Biochemistry and Molecular Biology, Medical College, Soochow University, Suzhou, Jiangsu China
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11
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Hu H, Chen X, Zhou C, Li B, Yang Y, Ying X, Mao Y, Zhang Y, Zhong J, Dai J, Yu H, Wu B, Li X, Wang T, Duan S. Aberrant methylation of mutL homolog 1 is associated with increased risk of non-small cell lung cancer. J Clin Lab Anal 2017; 32:e22370. [PMID: 29205508 DOI: 10.1002/jcla.22370] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 11/13/2017] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Non-small cell lung cancer (NSCLC) is a common malignant tumor. DNA hypermethylation in the promoter region has been served as a potential molecular marker for several tumors. The goal of the current study was to assess the diagnostic ability of mutL homolog 1 (MLH1) promoter methylation in NSCLC. METHODS A total of 111 NSCLC patients' paired tissue samples were obtained to explore the association between MLH1 promoter methylation and NSCLC by methylation-specific polymerase chain reaction (MSP) method. Public databases including The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) were used to verify our findings. RESULTS Our results showed a significantly higher MLH1 methylation frequency in tumor tissue samples than their paired adjacent tissues (P = .008). ROC curve indicated that MLH1MSP assay was a sensitive but not a specific method in the diagnosis for NSCLC (sensitivity = 0.964, specificity = 0.135, AUC = 0.550). And the association between the methylation level and clinical characteristics has no statistical significance. TCGA cohort evinced a higher methylation probability in tumor group compared with nontumor group (the mean β value: -0.449 [-0.467, -0.437] vs -0.466 [-0.472, -0.437], P = .011), which was consistent with our results. Meanwhile, an inverse correlation between MLH1 methylation and MLH1 expression was detected in TCGA and GEO databases. CONCLUSIONS The MSP method for MLH1 methylation was a sensitive but not a specific diagnostic method for NSCLC.
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Affiliation(s)
- Haochang Hu
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Xiaoying Chen
- Department of Medical Record, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Cong Zhou
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Bin Li
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Yong Yang
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Xiuru Ying
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Yiyi Mao
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Yihan Zhang
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Jie Zhong
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Jie Dai
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Hang Yu
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Boyi Wu
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Xiaodong Li
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Tiangong Wang
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Shiwei Duan
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
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12
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Han S, Yang X, Pan Y, Qi Q, Shen J, Fang H, Ji Z. L-securinine inhibits the proliferation of A549 lung cancer cells and promotes DKK1 promoter methylation. Oncol Lett 2017; 14:4243-4248. [PMID: 28943934 DOI: 10.3892/ol.2017.6693] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 06/02/2017] [Indexed: 12/25/2022] Open
Abstract
L-securinine is a natural product extracted and isolated from the leaf of dried Securinega suffruticosa. The aim of the present study was to explore the effects of L-securinine on proliferation, and the methylation profile of the dickkopf-related protein 1 (DKK1) gene in human lung cancer cells and fibroblasts. L-securinine was extracted, isolated and the structure was identified. The cytotoxicity of L-securinine in A549 cells was evaluated by Cell Counting Kit-8 assays. The expression and DNA methylation profile of DKK genes was analyzed by reverse transcription-quantitative polymerase chain reaction and bisulfite sequencing polymerase chain reaction, respectively. L-securinine inhibited the proliferation of lung cancer cells; the half-maximal inhibitory concentration values were 8.92, 4.73 and 3.81 µg/ml, at 24, 36 and 48 h post-treatment, respectively. DKK1, 2 and 3 expression was significantly increased in A549 cells compared with HLF-a cells. L-securinine induced the downregulation of DKK1 in A549 cells in a dose-dependent manner and induced methylation changes at CpG sites in the DKK1 promoter region. L-securinine may be a potential anticancer drug that mediates its effects by altering DKK1 gene methylation.
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Affiliation(s)
- Shuwen Han
- Department of Medical Oncology, Huzhou Central Hospital, Huzhou, Zhejiang 313000, P.R. China
| | - Xi Yang
- Department of Oncology, Wannan Medical College, Wuhu, Anhui 241000, P.R. China
| | - Yuefen Pan
- Department of Medical Oncology, Huzhou Central Hospital, Huzhou, Zhejiang 313000, P.R. China
| | - Quan Qi
- Department of Medical Oncology, Huzhou Central Hospital, Huzhou, Zhejiang 313000, P.R. China
| | - Junjun Shen
- Department of Medical Oncology, Huzhou Central Hospital, Huzhou, Zhejiang 313000, P.R. China
| | - Huifen Fang
- Department of Medical Oncology, Huzhou Central Hospital, Huzhou, Zhejiang 313000, P.R. China
| | - Zhaoning Ji
- The Cancer Center, Yijishan Hospital of Wannan Medical College, Wuhu, Anhui 241001, P.R. China
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13
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Costa-Pinheiro P, Montezuma D, Henrique R, Jerónimo C. Diagnostic and prognostic epigenetic biomarkers in cancer. Epigenomics 2015; 7:1003-15. [PMID: 26479312 DOI: 10.2217/epi.15.56] [Citation(s) in RCA: 135] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Growing cancer incidence and mortality worldwide demands development of accurate biomarkers to perfect detection, diagnosis, prognostication and monitoring. Urologic (prostate, bladder, kidney), lung, breast and colorectal cancers are the most common and despite major advances in their characterization, this has seldom translated into biomarkers amenable for clinical practice. Epigenetic alterations are innovative cancer biomarkers owing to stability, frequency, reversibility and accessibility in body fluids, entailing great potential of assay development to assist in patient management. Several studies identified putative epigenetic cancer biomarkers, some of which have been commercialized. However, large multicenter validation studies are required to foster translation to the clinics. Herein we review the most promising epigenetic detection, diagnostic, prognostic and predictive biomarkers for the most common cancers.
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Affiliation(s)
- Pedro Costa-Pinheiro
- Cancer Biology & Epigenetics Group - Research Center of Portuguese Oncology Institute - Porto (CI-IPOP), Porto, Portugal
| | - Diana Montezuma
- Cancer Biology & Epigenetics Group - Research Center of Portuguese Oncology Institute - Porto (CI-IPOP), Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute - Porto, Porto, Portugal
| | - Rui Henrique
- Cancer Biology & Epigenetics Group - Research Center of Portuguese Oncology Institute - Porto (CI-IPOP), Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute - Porto, Porto, Portugal.,Department of Pathology & Molecular Immunology, Institute of Biomedical Sciences Abel Salazar (ICBAS) - University of Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology & Epigenetics Group - Research Center of Portuguese Oncology Institute - Porto (CI-IPOP), Porto, Portugal.,Department of Pathology & Molecular Immunology, Institute of Biomedical Sciences Abel Salazar (ICBAS) - University of Porto, Portugal
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14
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Li W, Deng J, Wang SS, Ma L, Pei J, Zeng XX, Tang JX. Association of methylation of the RAR-β gene with cigarette smoking in non-small cell lung cancer with Southern-Central Chinese population. Asian Pac J Cancer Prev 2015; 15:10937-41. [PMID: 25605205 DOI: 10.7314/apjcp.2014.15.24.10937] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Pathogenesis of lung cancer is a complicated biological process including multiple genetic and epigenetic changes. Since cigarette smoking is confirmed as the most main risk factor of non-small cell lung cancer (NSCLC), the aim of this study was to determine whether tobacco exposure plays a role in gene methylation. Methylation of the RAR-β gene were detected using methylation-specific polymerase chain reaction in DNA from 167 newly diagnosed cases with NSCLC and corresponding 105 controls. A significant statistical association was found in the detection rate of the promoter methylation of RAR-β gene between NSCLC and controls (x2=166.01; p<0.01), and hypermethylation of the RAR-β gene was significantly associated with smoking status (p=0.038, p<0.05). No relationship was found between RAR-β gene methylation and pathologic staging including clinical stage, cell type, gender and drinking (p>0.05), and the methylation of RAR-β gene rate of NSCLC was slightly higher in stages III+IV (80.0%) than in I+II (70.8%). Similar results were obtained for methylation of the RAR-β gene between squamous cell carcinoma (77.9%) and other cell type lung cancer (73.9%). These results showed that the frequency of methylation increased gradually with the development of clinical stage in smoking-associated lung cancer patients, and tobacco smoke may be play a potential role in RAR-β gene methylation in the early pathogenesis and process in lung cancer, particularly squamous cell carcinoma. Aberrant promoter methylation is considered to be a promising marker of previous carcinogen exposure and cancer risk.
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Affiliation(s)
- Wen Li
- Key Laboratory of Green Packaging and Application of Biological Nanotechnology of Hunan Province, Hunan University of Technology, Zhuzhou, Hunan Province, P.R. China E-mail :
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15
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Targeting Chromatin-Mediated Transcriptional Control of Gene Expression in Non-Small Cell Lung Cancer Therapy: Preclinical Rationale and Clinical Results. Drugs 2015; 75:1757-71. [DOI: 10.1007/s40265-015-0461-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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16
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Harada H, Miyamoto K, Yamashita Y, Taniyama K, Mihara K, Nishimura M, Okada M. Prognostic signature of protocadherin 10 methylation in curatively resected pathological stage I non-small-cell lung cancer. Cancer Med 2015; 4:1536-46. [PMID: 26276761 PMCID: PMC4618624 DOI: 10.1002/cam4.507] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2015] [Revised: 06/13/2015] [Accepted: 07/14/2015] [Indexed: 12/31/2022] Open
Abstract
Although curative resection is the current treatment of choice for localized non-small-cell lung cancer (NSCLC), patients show a wide spectrum of survival even after complete resection of pathological stage I NSCLC. Thus, identifying molecular biomarkers that help to accurately select patients at high risk of relapse is an important key to improving the treatment strategy. The purpose of this study was to evaluate the prognostic signature of protocadherin 10 (PCDH10) promoter methylation in curatively resected pathological stage I NSCLC. Using methylation-specific polymerase chain reaction assays, methylation of PCDH10 promoter was assessed in cancer tissues of 109 patients who underwent curative resection of pathological stage I NSCLC. Associations between PCDH10 methylation status and disease outcome was analyzed. PCDH10 promoter methylation was detected in 46/109 patients (42.2%). Patients with methylated PCDH10 showed significantly worse recurrence-free, overall, and disease-specific survival compared with those without methylation (P < 0.0001, P = 0.0004, P = 0.0002, respectively). Multivariate Cox proportional hazard regression analysis revealed that adjusted hazard ratios of methylated PCDH10 were 5.159 for recurrence-free, 1.817 for overall, and 5.478 for disease-specific survival (P = 0.0005, P = 0.1475, P = 0.0109, respectively). The pattern of recurrence was not significantly different between patients with and without PCDH10 methylation (P = 0.5074). PCDH10 methylation is a potential biomarker that predicts a poor prognosis after curative resection of pathological stage I NSCLC. Assessment of PCDH10 methylation status might assist in patient stratification for determining an appropriate adjuvant treatment and follow-up strategy.
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Affiliation(s)
- Hiroaki Harada
- Department of Respiratory Surgery, National Hospital Organization Kure Medical Center/Chugoku Cancer Center, 3-1 Aoyama-cho, Kure, Hiroshima, 737-0023, Japan.,Institute for Clinical Research, National Hospital Organization Kure Medical Center/Chugoku Cancer Center, 3-1 Aoyama-cho, Kure, Hiroshima, 737-0023, Japan
| | - Kazuaki Miyamoto
- Institute for Clinical Research, National Hospital Organization Kure Medical Center/Chugoku Cancer Center, 3-1 Aoyama-cho, Kure, Hiroshima, 737-0023, Japan.,Department of Surgery, National Hospital Organization Higashihiroshima Medical Center, 513 Teraya Saijyo-cho, Higashihiroshima, Hiroshima, 739-0041, Japan
| | - Yoshinori Yamashita
- Department of Respiratory Surgery, National Hospital Organization Kure Medical Center/Chugoku Cancer Center, 3-1 Aoyama-cho, Kure, Hiroshima, 737-0023, Japan.,Institute for Clinical Research, National Hospital Organization Kure Medical Center/Chugoku Cancer Center, 3-1 Aoyama-cho, Kure, Hiroshima, 737-0023, Japan
| | - Kiyomi Taniyama
- Institute for Clinical Research, National Hospital Organization Kure Medical Center/Chugoku Cancer Center, 3-1 Aoyama-cho, Kure, Hiroshima, 737-0023, Japan
| | - Kazuko Mihara
- Institute for Clinical Research, National Hospital Organization Kure Medical Center/Chugoku Cancer Center, 3-1 Aoyama-cho, Kure, Hiroshima, 737-0023, Japan
| | - Mitsuki Nishimura
- Institute for Clinical Research, National Hospital Organization Kure Medical Center/Chugoku Cancer Center, 3-1 Aoyama-cho, Kure, Hiroshima, 737-0023, Japan
| | - Morihito Okada
- Department of Surgical Oncology, Research Institute for Radiation Biology and Medicine, Graduate School of Biomedical Science, Hiroshima University, 1-2-3 Kasumi Minami-ku, Hiroshima, Hiroshima, 734-8551, Japan
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17
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Methylated DLX4 Predicts Response to Pathologic Stage I Non-Small Cell Lung Cancer Resection. Ann Thorac Surg 2015; 99:1746-54. [DOI: 10.1016/j.athoracsur.2014.12.058] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Revised: 12/05/2014] [Accepted: 12/16/2014] [Indexed: 12/31/2022]
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18
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Abstract
Lung cancer is the most frequently occurring cancer in the world and continually leads in mortality among cancers. The overall 5-year survival rate for lung cancer has risen only 4% (from 12% to 16%) over the past 4 decades, and late diagnosis is a major obstacle in improving lung cancer prognosis. Survival of patients undergoing lung resection is greater than 80%, suggesting that early detection and diagnosis of cancers before they become inoperable and lethal will greatly improve mortality. Lung cancer biomarkers can be used for screening, detection, diagnosis, prognosis, prediction, stratification, therapy response monitoring, and so on. This review focuses on noninvasive diagnostic and prognostic biomarkers. For that purpose, our discussion in this review will focus on biological fluid-based biomarkers. The body fluids include blood (serum or plasma), sputum, saliva, BAL, pleural effusion, and VOC. Since it is rich in different cellular and molecular elements and is one of the most convenient and routine clinical procedures, serum or plasma is the main source for the development and validation of many noninvasive biomarkers. In terms of molecular aspects, the most widely validated ones are proteins, some of which are used in the clinical sector, though in limited accessory purposes. We will also discuss the lung cancer (protein) biomarkers in clinical trials and currently in the validation phase with hundreds of samples. After proteins, we will discuss microRNAs, methylated DNA, and circulating tumor cells, which are being vigorously developed and validated as potential lung cancer biomarkers. The main aim of this review is to provide researchers and clinicians with an understanding of the potential noninvasive lung cancer biomarkers in biological fluids that have recently been discovered.
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19
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Nawaz I, Qiu X, Wu H, Li Y, Fan Y, Hu LF, Zhou Q, Ernberg I. Development of a multiplex methylation specific PCR suitable for (early) detection of non-small cell lung cancer. Epigenetics 2014; 9:1138-48. [PMID: 24937636 DOI: 10.4161/epi.29499] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Lung cancer is a worldwide health problem and a leading cause of cancer-related deaths. Silencing of potential tumor suppressor genes (TSGs) by aberrant promoter methylation is an early event in the initiation and development of cancer. Thus, methylated cancer type-specific TSGs in DNA can serve as useful biomarkers for early cancer detection. We have now developed a "Multiplex Methylation Specific PCR" (MMSP) assay for analysis of the methylation status of multiple potential TSGs by a single PCR reaction. This method will be useful for early diagnosis and treatment outcome studies of non-small cell lung cancer (NSCLC). Genome-wide CpG methylation and expression microarrays were performed on lung cancer tissues and matched distant non-cancerous tissues from three NSCLC patients from China. Thirty-eight potential TSGs were selected and analyzed by methylation PCR on bisulfite treated DNA. On the basis of sensitivity and specificity, six marker genes, HOXA9, TBX5, PITX2, CALCA, RASSF1A, and DLEC1, were selected to establish the MMSP assay. This assay was then used to analyze lung cancer tissues and matched distant non-cancerous tissues from 70 patients with NSCLC, as well as 24 patients with benign pulmonary lesion as controls. The sensitivity of the assay was 99% (69/70). HOXA9 and TBX5 were the 2 most sensitive marker genes: 87% (61/70) and 84% (59/70), respectively. RASSF1A and DLEC1 showed the highest specificity at 99% (69/70). Using the criterion of identifying at least any two methylated marker genes, 61/70 cancer samples were positive, corresponding to a sensitivity of 87% and a specificity of 94%. Early stage I or II NSCLC could even be detected with a 100% specificity and 86% sensitivity. In conclusion, MMSP has the potential to be developed into a population-based screening tool and can be useful for early diagnosis of NSCLC. It might also be suitable for monitoring treatment outcome and recurrence.
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Affiliation(s)
- Imran Nawaz
- Department of Microbiology; Tumor and Cell Biology; Karolinska Institute; Stockholm, Sweden; Department of Microbiology; Faculty of Life Sciences; University of Balochistan; Quetta, Pakistan
| | - Xiaoming Qiu
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment; Tianjin Lung Cancer Institute; Tianjin Medical University General Hospital; Tianjin, PR China
| | - Heng Wu
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment; Tianjin Lung Cancer Institute; Tianjin Medical University General Hospital; Tianjin, PR China
| | - Yang Li
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment; Tianjin Lung Cancer Institute; Tianjin Medical University General Hospital; Tianjin, PR China
| | - Yaguang Fan
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment; Tianjin Lung Cancer Institute; Tianjin Medical University General Hospital; Tianjin, PR China
| | - Li-Fu Hu
- Department of Microbiology; Tumor and Cell Biology; Karolinska Institute; Stockholm, Sweden
| | - Qinghua Zhou
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment; Tianjin Lung Cancer Institute; Tianjin Medical University General Hospital; Tianjin, PR China
| | - Ingemar Ernberg
- Department of Microbiology; Tumor and Cell Biology; Karolinska Institute; Stockholm, Sweden
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